Yuri P. Blagoi

The rotamerization of conformers of glycine isolated in inert gas matrices. An infrared spectroscopic study

Abstract The infrared spectra of glycine isolated in Ne, Ar and Kr matrices have been measured. The matrix-isolated glycine is shown to be in the molecular form. The spectral manifestations, both conformational and site splitting, are separated. Three different conformers of glycine have been identified experimentally for the first time. It is shown that during the deposition of the samples the substrate temperature must be lowered to 13 K — this is a decisive factor permitting fixation of a complete set of glycine conformers in an inert matrix. The relative energies of the three glycine conformers are estimated to be 0, 1.3–1.6 and 0.9–1.5 kcal/mol.

The rotamerization of conformers of glycine isolated in inert gas matrices. An infrared spectroscopic study (Chem. Phys. Letters 232 (1995) 141)

The infrared spectra of glycine isolated in Ne, Ar and Kr matrices have been measured. The matrix-isolated glycine is shown to be in the molecular form. The spectral manifestations, both conformational and site splitting, are separated. Three different conformers ofglycine have been identified experimentally for the first time. It is shown that during the deposition of the samples the substrate temperature must be lowered to 13 K this is a decisive factor permitting fixation of a complete set of glycine conformers in an inert matrix. The relative energies of the three glycine conformers are estimated to be 0, 1.3-1.6 and 0.9-1.5 kcal/mol.

Studies of formation of bivalent copper complexes with native and denatured DNA

The formation of Cu2+ complexes with native and denatured DNA is studied by the methods of differential UV spectroscopy, CD spectroscopy, and viscometry. On ion binding to the bases of native DNA the latter transforms into a new conformation. This transition is accompanied with a sharp increase in UV absorption and a decrease in the intrinsic viscosity though the high degree of helicity persists. Possible sites of Cu2+ ion binding on DNA of various conformations are found along with corresponding constants of complex formation.

Studies of bivalent copper ion binding to poly C

Ultraviolet differential spectra of single-stranded poly C, taken in the presence of Cu2+ ions, are studied at various ionic strengths and temperatures. Coordinational and conformational components of these spectra are obtained. The Cu2+ ion coordination site on the polynucleotide bases is found to be N(3) and possibly O(2). The direction of the poly C absorption band shift due to ion binding and conformational transitions is established. At low ionic strengths of the solution Cu2+ ions cause the helical parts of poly C to melt. At high ones the formation of double-stranded parts was observed in addition to the above effect. The calculated concentration dependences of ion-poly C bases association constants show that binding is cooperative at any ionic strength.

Interaction of divalent metal ions with poly(riboinosinic acid)

Methods of differential UV and visible spectroscopy are used to study the interaction of Mg 2+ , Ca 2+ , Ma 2+ and Cu 2+ ions with four (4 × 1), and single-stranded poly 1 is solutions with 1 mol.l -1 Na + . Up to concentrations of about 0.1 mol.l -1 Mt 2+ , Mg 3+ and Ca 2+ ions do not bind to hetereatoms of hypoxanthine of 4 × 1, Cu 5+ ions interact with N7 and/or N1 and possibly with O6 through the water molecule of the hydrate shell of the ion. It is likely that the interaction with O6 causes enolization of the hypoxanthine. N1 deprotonation and as a result, this leads to the melting of the four-stranded helix. In single-stranded chains, Cu 2+ ions induce the formation of compact particles which have the effective radii r e ≃ 100 A. The Ma 2+ -induced differential spectra are simalar to those observed in the presence of Cu 2+ ions but in the case of Mn 2+ they occur at concentrations about two orders of magnitude higher. In contrast to the positive cooperativity of the Cu 2+ binding to bases of single-stranded poly I, their interaction with 5 × 1 has the negative cooperativity.

Ni2+ ion effect on conformational transitions in triple helix of polyA-2polyU

Recently data were published on the participation of nucleic acids with non Watson-Crick pairing (of duplexes, triplexes and quadruplexes) in biological processes. It is of interest to study nucleic acid interactions with metal ions inducing mutagenesis and carcinogenesis.

Mg2+ ion effect on phase equilibrium in polyA·polyU and polyA·2polyU

Noncanonical structures of nucleic acids are involved in main biological reactions. To identify cell mechanisms of structural reconstructions in nucleic acids is a key problem of molecular biology. One of the factors having an influence on the stability of different structures is the ion environment. Na+ effects on structural transitions in such molecules as polyApolyU are well studied and phase diagrams are built [1]. The present work was aimed at building of the complete phase diagram for polyApolyU, polyA-2polyU complexes with Mg2+ at different ionic strengths.

Effects of divalent metal ions on secondary and tertiary structures of polyriboinosinic acid

Interest in noncanonical multichain helices (NMH) is aroused due to their taking part in biological processes. It is interesting to study effects of metal ions (Me2+) on NMH structures.

Interaction between DNA and biometal ions. Variations of structural and macromolecular parameters

The interaction of Mg2+, Ca2+, Mn2+, and Cu2+ ions with the DNA macromolecule is studied in a wide range of ionic strengths, 2 · 10−4 to 10−1 mol · 1−1. It is shown that the observed considerable changes in the intrinsic viscosity and the excluded volume parameter of DNA are due to the screening of the phosphate groups and nitrogen bases of DNA during the direct binding of the ions. The bivalent ion binding to DNA leads to suppression of the effects of the long-range interactions in the macromolecules at concentrations two or three orders of magnitude lower than those for monovalent ions. The intrinsic viscosity and the excluded volume parameter are universally dependent on the ion binding degree.

Structural variations of DNA + Mn2+ complexes during helix-coil transition

Etude par diffusion de la lumiere et spectrometrie UV. Le domaine de transition se trouve autour de 0,5°C